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In that case, Anderson will have to take a look. FYI: The PALM Wiki page probably includes a more complete list of the full set of available options: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask] From: Darren Campbell <[log in to unmask]> Date: Friday, March 1, 2019 at 1:24 PM To: "Harms, Michael" <[log in to unmask]> Cc: FSL - FMRIB's Software Library <[log in to unmask]>, "Anderson M. Winkler" <[log in to unmask]>, "[log in to unmask]" <[log in to unmask]>, "[log in to unmask]" <[log in to unmask]> Subject: Re: Palm feedback: # rows does not match # obs in data, but it does :( Hi Michael et al., Thanks for the quick response. I did not see the specific transpose data command in the palm -help list, so I inserted transposedata immediately after the -i information inputs. the transposedata did not work (see feedback below). Thanks again. Other suggestions? Darren Feedback With transposedata inserted (in case it is diagnostically helpful) Running PALM alpha112 using Octave 4.2.2 with the following options: -i ./HCP_subjects/Y_left.func.gii -i ./HCP_subjects/Y_right.func.gii -transposedata -d ./HCP_subjects/Progs/Design.mat -t ./HCP_subjects/Progs/DesignGrpContr.con -o dense_cortical_Results -n 1000 -corrcon -corrmod -logp -accel tail -nouncorrected -T -tfce2D -s ./HCP_subjects/L_midthickness.surf.gii -s ./HCP_subjects/R_midthickness.surf.gii Found FSL in /usr/local/fsl Found FreeSurfer in /usr/local/freesurfer Found HCP Workbench executable in /home/brain/workbench/bin_linux64/wb_command Loading surface 1/2: ./HCP_subjects/L_midthickness.surf.gii warning: xml_findstr is not compiled for your platform. This will result in a slowdown of the XML parsing. Loading surface 2/2: ./HCP_subjects/R_midthickness.surf.gii Reading input 1/2: ./HCP_subjects/Y_left.func.gii Error using palm_takeargs (/home/brain/PALM-master/palm_takeargs.m:1694) Surface file does not match the input data: - Surface file 1 has 32492 vertices and 64980 faces (./HCP_subjects/L_midthickness.surf.gii) - Input data file 1 has 190 points (./HCP_subjects/Y_left.func.gii) Error in palm_core (/home/brain/PALM-master/palm_core.m:33->palm_takeargs) Error in palm (/home/brain/PALM-master/palm.m:81->palm_core) Dr. Darren Campbell Associate Professor Department of Psychology Nipissing University Office: H236 Phone: 705-474-3450 Ext. 4524 Lab: A222F On Fri, Mar 1, 2019 at 2:10 PM Harms, Michael <[log in to unmask]<mailto:[log in to unmask]>> wrote: Try using the -tranposedata flag. If that doesn’t solve the problem, Anderson will need to comment. -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask]<mailto:[log in to unmask]> From: Darren Campbell <[log in to unmask]<mailto:[log in to unmask]>> Date: Friday, March 1, 2019 at 1:04 PM To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Cc: "Anderson M. Winkler" <[log in to unmask]<mailto:[log in to unmask]>>, "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>>, "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>>, "Harms, Michael" <[log in to unmask]<mailto:[log in to unmask]>>, Darren Campbell <[log in to unmask]<mailto:[log in to unmask]>> Subject: Palm feedback: # rows does not match # obs in data, but it does :( Hi Following the TFCE palm analyses example (Exploring the H C 2018 Practical 11: Task fMRI) on a subsample of the HCP data, I successfully ran the subcortical analyses command (# rows = # obs). But, when I ran the parallel command for the lateralized cortical analyses, I received an error (# rows does not match # obs). The wb_command -file-information on two cortical .gii files indicated that there were the correct # of obs (192). I have pasted the error and other potentially relevant info below. Any suggestions? Thanks. Darren P.S. I am email rather than posting due to posting difficulties. # Step 5 - lateralized cortical analyses palm -i ./HCP_subjects/Y_left.func.gii -i ./HCP_subjects/Y_right.func.gii -d ./HCP_subjects/Progs/Design.mat -t ./HCP_subjects/Progs/DesignGrpContr.con -o dense_cortical_Results -n 1000 -corrcon -corrmod -logp -accel tail -nouncorrected -T -tfce2D -s ./HCP_subjects/L_midthickness.surf.gii -s ./HCP_subjects/R_midthickness.surf.gii Running PALM alpha112 using Octave 4.2.2 with the following options: -i ./HCP_subjects/Y_left.func.gii -i ./HCP_subjects/Y_right.func.gii -d ./HCP_subjects/Progs/Design.mat -t ./HCP_subjects/Progs/DesignGrpContr.con -o dense_cortical_Results -n 1000 -corrcon -corrmod -logp -accel tail -nouncorrected -T -tfce2D -s ./HCP_subjects/L_midthickness.surf.gii -s ./HCP_subjects/R_midthickness.surf.gii Found FSL in /usr/local/fsl Found FreeSurfer in /usr/local/freesurfer Found HCP Workbench executable in /home/brain/workbench/bin_linux64/wb_command Loading surface 1/2: ./HCP_subjects/L_midthickness.surf.gii warning: xml_findstr is not compiled for your platform. This will result in a slowdown of the XML parsing. Loading surface 2/2: ./HCP_subjects/R_midthickness.surf.gii Reading input 1/2: ./HCP_subjects/Y_left.func.gii Reading input 2/2: ./HCP_subjects/Y_right.func.gii Reading design matrix and contrasts. Error using palm_takeargs (/home/brain/PALM-master/palm_takeargs.m:2053) The number of rows in the design matrix does not match the number of observations in the data. - Rows in the matrix: 192 - Observations in the data: 190 In file ./HCP_subjects/Progs/Design.mat Error in palm_core (/home/brain/PALM-master/palm_core.m:33->palm_takeargs) Error in palm (/home/brain/PALM-master/palm.m:81->palm_core) DesignGrpContr.con /NumWaves 3 /NumPoints 3 /Matrix 1 -1 0 1 0 -1 0 1 -1 Design.mat /NumWaves 3 /NumPoints 192 /Matrix 1 0 0 1 0 0 . . . 1 0 0 0 1 0 (Line 68 - my notation for you not in file) 0 1 0 . . . 0 1 0 0 0 1 0 0 1 (Line 132) . . . 0 0 1 0 0 1 (Line 195) One of the Data Files (Y_left.func.gii) wb_command -file-information ./HCP_subjects/Y192_left.func.gii Name: ./HCP_subjects/Y192_left.func.gii Type: Metric Structure: CortexLeft Data Size: 24.95 Megabytes Maps to Surface: true Maps to Volume: false Maps with LabelTable: false Maps with Palette: true All Map Palettes Equal: true Map Interval Units: NIFTI_UNITS_UNKNOWN Number of Maps: 192 Number of Vertices: 32492 Map Minimum Maximum Mean Sample Dev % Positive % Negative Inf/NaN Map Name 1 -245.956 369.890 4.569 54.864 49.649 41.746 0 #1 . . . 191 -277.772 335.542 -15.126 60.584 33.316 58.079 0 #191 192 -219.324 351.132 4.193 46.065 46.571 44.823 0 #192 Dr. Darren Campbell Associate Professor Department of Psychology Nipissing University Office: H236 Phone: 705-474-3450 Ext. 4524 Lab: A222F ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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